public IEnumerable <PeptideDocNode> CreatePeptideDocNodes(SrmSettings settings, bool useFilter, Target peptideSequence)
{
PeptideSettings pepSettings = settings.PeptideSettings;
DigestSettings digest = pepSettings.DigestSettings;
IPeptideFilter filter = (useFilter ? settings : PeptideFilter.UNFILTERED);
int? maxLen = null, minLen = null;
var pick = pepSettings.Libraries.Pick;
if (useFilter && pick != PeptidePick.library && pick != PeptidePick.either)
{
// CONSIDER(brendanx): It should be possible to get min and max length from libraries
maxLen = pepSettings.Filter.MaxPeptideLength;
minLen = pepSettings.Filter.MinPeptideLength;
}
foreach (var peptide in pepSettings.Enzyme.Digest(this, digest, maxLen, minLen))
{
if (null != peptideSequence && !Equals(peptideSequence, peptide.Target))
{
continue;
}
foreach (var nodePep in peptide.CreateDocNodes(settings, filter))
{
yield return(nodePep);
}
}
}
public IEnumerable <PeptideDocNode> CreatePeptideDocNodes(SrmSettings settings, bool useFilter, string peptideSequence)
{
PeptideSettings pepSettings = settings.PeptideSettings;
DigestSettings digest = pepSettings.DigestSettings;
IPeptideFilter filter = (useFilter ? settings : PeptideFilter.UNFILTERED);
foreach (var peptide in pepSettings.Enzyme.Digest(this, digest))
{
if (null != peptideSequence && peptideSequence != peptide.Sequence)
{
continue;
}
foreach (var nodePep in peptide.CreateDocNodes(settings, filter))
{
yield return(nodePep);
}
}
}
public IEnumerable <PeptideDocNode> CreateDocNodes(SrmSettings settings, IPeptideFilter filter, IVariableModFilter filterVariableMod = null)
{
int maxModCount = filter.MaxVariableMods ?? settings.PeptideSettings.Modifications.MaxVariableMods;
// Always return the unmodified peptide doc node first
var nodePepUnmod = new PeptideDocNode(this);
bool allowVariableMods;
if (filter.Accept(settings, this, null, out allowVariableMods))
{
yield return(nodePepUnmod);
}
// Stop if no variable modifications are allowed for this peptide.
if (!allowVariableMods || maxModCount == 0)
{
yield break;
}
// First build a list of the amino acids in this peptide which can be modified,
// and the modifications which apply to them.
var listListMods = CalcApplicableMods(settings, filterVariableMod);
// If no applicable modifications were found, return a single DocNode for the
// peptide passed in
if (listListMods == null)
{
yield break;
}
maxModCount = Math.Min(maxModCount, listListMods.Count);
for (int modCount = 1; modCount <= maxModCount; modCount++)
{
var modStateMachine = new VariableModStateMachine(nodePepUnmod, modCount, listListMods);
foreach (var nodePep in modStateMachine.GetStates())
{
if (filter.Accept(settings, nodePep.Peptide, nodePep.ExplicitMods, out allowVariableMods))
{
yield return(nodePep);
}
}
}
}
public IEnumerable <PeptideDocNode> CreateDocNodes(SrmSettings settings, IPeptideFilter filter)
{
int maxModCount = filter.MaxVariableMods ?? settings.PeptideSettings.Modifications.MaxVariableMods;
// Always return the unmodified peptide doc node first
var nodePepUnmod = new PeptideDocNode(this);
bool allowVariableMods;
if (filter.Accept(settings, this, null, out allowVariableMods))
{
yield return(nodePepUnmod);
}
// Stop if no variable modifications are allowed for this peptide.
if (!allowVariableMods || maxModCount == 0)
{
yield break;
}
// First build a list of the amino acids in this peptide which can be modified,
// and the modifications which apply to them.
List <KeyValuePair <IList <StaticMod>, int> > listListMods = null;
var mods = settings.PeptideSettings.Modifications;
// Nothing to do, if no variable mods in the document
if (mods.HasVariableModifications)
{
// Enumerate each amino acid in the sequence
int len = Sequence.Length;
for (int i = 0; i < len; i++)
{
char aa = Sequence[i];
// Test each modification to see if it applies
foreach (var mod in mods.VariableModifications)
{
// If the modification does apply, store it in the list
if (mod.IsMod(aa, i, len))
{
if (listListMods == null)
{
listListMods = new List <KeyValuePair <IList <StaticMod>, int> >();
}
if (listListMods.Count == 0 || listListMods[listListMods.Count - 1].Value != i)
{
listListMods.Add(new KeyValuePair <IList <StaticMod>, int>(new List <StaticMod>(), i));
}
listListMods[listListMods.Count - 1].Key.Add(mod);
}
}
}
}
// If no applicable modifications were found, return a single DocNode for the
// peptide passed in
if (listListMods == null)
{
yield break;
}
maxModCount = Math.Min(maxModCount, listListMods.Count);
for (int modCount = 1; modCount <= maxModCount; modCount++)
{
var modStateMachine = new VariableModStateMachine(nodePepUnmod, modCount, listListMods);
foreach (var nodePep in modStateMachine.GetStates())
{
if (filter.Accept(settings, nodePep.Peptide, nodePep.ExplicitMods, out allowVariableMods))
{
yield return(nodePep);
}
}
}
}
public IEnumerable <PeptideDocNode> GetPeptideNodes(SrmSettings settings, bool useFilter)
{
// FASTA sequences can generate a comprehensive list of available peptides.
FastaSequence fastaSeq = Id as FastaSequence;
if (fastaSeq != null)
{
foreach (PeptideDocNode nodePep in fastaSeq.CreatePeptideDocNodes(settings, useFilter, null))
{
yield return(nodePep);
}
}
// Peptide lists without variable modifications just return their existing children.
else if (!settings.PeptideSettings.Modifications.HasVariableModifications)
{
foreach (PeptideDocNode nodePep in Children)
{
if (!nodePep.HasVariableMods)
{
yield return(nodePep);
}
}
}
// If there are variable modifications, fill out the available list.
else
{
var setNonExplicit = new HashSet <Peptide>();
IPeptideFilter filter = (useFilter ? settings : PeptideFilter.UNFILTERED);
foreach (PeptideDocNode nodePep in Children)
{
if (nodePep.Peptide.IsCustomIon) // Modifications mean nothing to custom ions
{
yield return(nodePep);
}
else if (nodePep.HasExplicitMods && !nodePep.HasVariableMods)
{
yield return(nodePep);
}
else if (!setNonExplicit.Contains(nodePep.Peptide))
{
bool returnedResult = false;
var peptide = nodePep.Peptide;
// The peptide will be returned as the Id of the unmodified instance of this
// peptide. If the peptide DocNode is explicitly modified this will cause
// two nodes in the tree to have the same Id. So, use a copy instead.
if (nodePep.HasExplicitMods)
{
peptide = (Peptide)peptide.Copy();
}
foreach (PeptideDocNode nodePepResult in peptide.CreateDocNodes(settings, filter))
{
yield return(nodePepResult);
returnedResult = true;
}
// Make sure the peptide is not removed due to filtering
if (!returnedResult)
{
yield return(nodePep);
}
setNonExplicit.Add(nodePep.Peptide);
}
}
}
}
